| A_palsy_qege |
| ID: | 1497387166 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 568 (533) | ||
| Sequences: | 35947 (25434.7) | ||
| Seq/Len: | 67.443 | ||
| Nf(neff/√len): | 1101.7 |
HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 67.443).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 173_S | 190_E | 4.666 | 1.00 |
| 410_V | 444_G | 3.943 | 1.00 |
| 480_V | 527_H | 3.554 | 1.00 |
| 192_S | 419_K | 3.444 | 1.00 |
| 391_T | 413_K | 3.054 | 1.00 |
| 54_E | 90_L | 3.043 | 1.00 |
| 424_N | 427_A | 3.006 | 1.00 |
| 70_P | 96_T | 3.000 | 1.00 |
| 409_R | 439_H | 2.998 | 1.00 |
| 50_Q | 90_L | 2.996 | 1.00 |
| 120_L | 178_L | 2.989 | 1.00 |
| 395_V | 411_Q | 2.840 | 1.00 |
| 69_D | 124_P | 2.837 | 1.00 |
| 445_F | 452_T | 2.801 | 1.00 |
| 65_L | 93_F | 2.754 | 1.00 |
| 72_F | 123_H | 2.616 | 1.00 |
| 68_G | 172_D | 2.547 | 1.00 |
| 59_G | 63_L | 2.442 | 1.00 |
| 407_I | 443_L | 2.380 | 1.00 |
| 459_D | 557_R | 2.373 | 1.00 |
| 272_N | 275_F | 2.365 | 1.00 |
| 477_A | 505_L | 2.351 | 1.00 |
| 23_T | 50_Q | 2.329 | 1.00 |
| 25_A | 29_T | 2.310 | 1.00 |
| 56_V | 83_T | 2.282 | 1.00 |
| 258_D | 262_R | 2.277 | 1.00 |
| 396_N | 400_E | 2.272 | 1.00 |
| 68_G | 419_K | 2.211 | 1.00 |
| 116_H | 185_M | 2.186 | 1.00 |
| 29_T | 32_L | 2.176 | 1.00 |
| 192_S | 195_S | 2.172 | 1.00 |
| 407_I | 454_T | 2.169 | 1.00 |
| 462_I | 467_N | 2.112 | 1.00 |
| 169_A | 172_D | 2.095 | 1.00 |
| 425_D | 429_Q | 2.092 | 1.00 |
| 67_A | 172_D | 2.090 | 1.00 |
| 50_Q | 54_E | 2.088 | 1.00 |
| 47_A | 51_G | 2.062 | 1.00 |
| 33_T | 43_T | 2.022 | 1.00 |
| 66_K | 69_D | 1.960 | 1.00 |
| 120_L | 424_N | 1.957 | 1.00 |
| 479_E | 531_K | 1.924 | 1.00 |
| 25_A | 28_T | 1.923 | 1.00 |
| 176_F | 422_Y | 1.920 | 1.00 |
| 478_E | 485_T | 1.915 | 1.00 |
| 88_C | 93_F | 1.914 | 1.00 |
| 31_G | 47_A | 1.901 | 1.00 |
| 411_Q | 439_H | 1.891 | 1.00 |
| 108_N | 113_K | 1.881 | 1.00 |
| 53_A | 90_L | 1.879 | 1.00 |
| 508_T | 547_F | 1.878 | 1.00 |
| 173_S | 419_K | 1.863 | 1.00 |
| 326_V | 344_F | 1.861 | 1.00 |
| 65_L | 69_D | 1.847 | 1.00 |
| 122_E | 423_R | 1.843 | 1.00 |
| 195_S | 337_S | 1.838 | 1.00 |
| 307_P | 311_H | 1.836 | 1.00 |
| 478_E | 486_S | 1.829 | 1.00 |
| 394_I | 444_G | 1.825 | 1.00 |
| 16_Q | 24_E | 1.822 | 1.00 |
| 70_P | 94_V | 1.803 | 1.00 |
| 70_P | 176_F | 1.796 | 1.00 |
| 341_V | 392_I | 1.789 | 1.00 |
| 178_L | 188_C | 1.777 | 1.00 |
| 45_S | 48_Q | 1.771 | 1.00 |
| 24_E | 28_T | 1.769 | 1.00 |
| 213_D | 296_T | 1.762 | 1.00 |
| 54_E | 58_T | 1.746 | 1.00 |
| 506_F | 561_K | 1.742 | 1.00 |
| 118_W | 123_H | 1.733 | 1.00 |
| 213_D | 266_T | 1.724 | 1.00 |
| 84_A | 127_L | 1.717 | 1.00 |
| 17_T | 20_D | 1.699 | 1.00 |
| 72_F | 98_V | 1.686 | 1.00 |
| 87_A | 91_G | 1.678 | 1.00 |
| 392_I | 412_I | 1.677 | 1.00 |
| 52_D | 83_T | 1.668 | 1.00 |
| 171_D | 194_R | 1.663 | 1.00 |
| 264_R | 294_A | 1.661 | 1.00 |
| 444_G | 453_L | 1.656 | 1.00 |
| 556_E | 559_Q | 1.652 | 1.00 |
| 461_I | 470_N | 1.650 | 1.00 |
| 485_T | 549_K | 1.649 | 1.00 |
| 205_A | 388_P | 1.647 | 1.00 |
| 427_A | 430_E | 1.646 | 1.00 |
| 403_P | 406_H | 1.644 | 1.00 |
| 44_Q | 83_T | 1.641 | 1.00 |
| 413_K | 437_W | 1.640 | 1.00 |
| 506_F | 560_L | 1.626 | 1.00 |
| 89_V | 174_V | 1.625 | 1.00 |
| 445_F | 454_T | 1.617 | 1.00 |
| 447_H | 452_T | 1.611 | 1.00 |
| 340_V | 412_I | 1.610 | 1.00 |
| 259_W | 263_Y | 1.608 | 1.00 |
| 235_V | 238_G | 1.598 | 1.00 |
| 246_T | 249_F | 1.592 | 1.00 |
| 382_E | 452_T | 1.589 | 1.00 |
| 426_E | 430_E | 1.589 | 1.00 |
| 23_T | 90_L | 1.584 | 1.00 |
| 171_D | 192_S | 1.576 | 1.00 |
| 538_R | 541_P | 1.575 | 1.00 |
| 73_F | 84_A | 1.566 | 1.00 |
| 447_H | 450_R | 1.563 | 1.00 |
| 115_H | 119_K | 1.555 | 1.00 |
| 252_Q | 255_R | 1.543 | 1.00 |
| 94_V | 173_S | 1.539 | 1.00 |
| 56_V | 87_A | 1.536 | 1.00 |
| 52_D | 80_A | 1.528 | 1.00 |
| 418_M | 432_F | 1.517 | 1.00 |
| 306_V | 309_T | 1.514 | 1.00 |
| 44_Q | 79_H | 1.513 | 1.00 |
| 195_S | 417_T | 1.509 | 1.00 |
| 527_H | 531_K | 1.499 | 1.00 |
| 120_L | 185_M | 1.489 | 1.00 |
| 76_S | 129_D | 1.482 | 1.00 |
| 463_I | 468_Y | 1.481 | 1.00 |
| 71_V | 93_F | 1.475 | 1.00 |
| 385_K | 450_R | 1.464 | 1.00 |
| 484_E | 510_K | 1.462 | 1.00 |
| 198_A | 389_G | 1.461 | 1.00 |
| 443_L | 457_E | 1.446 | 1.00 |
| 168_A | 172_D | 1.435 | 1.00 |
| 446_L | 451_L | 1.426 | 1.00 |
| 474_E | 488_V | 1.426 | 1.00 |
| 61_R | 91_G | 1.423 | 1.00 |
| 50_Q | 163_T | 1.416 | 1.00 |
| 404_E | 446_L | 1.414 | 1.00 |
| 396_N | 402_L | 1.393 | 0.99 |
| 194_R | 415_P | 1.390 | 0.99 |
| 393_R | 411_Q | 1.385 | 0.99 |
| 311_H | 315_H | 1.380 | 0.99 |
| 299_I | 330_A | 1.378 | 0.99 |
| 533_G | 536_A | 1.378 | 0.99 |
| 507_F | 543_Q | 1.377 | 0.99 |
| 460_M | 469_H | 1.377 | 0.99 |
| 190_E | 422_Y | 1.376 | 0.99 |
| 271_P | 275_F | 1.375 | 0.99 |
| 98_V | 114_L | 1.374 | 0.99 |
| 427_A | 431_V | 1.366 | 0.99 |
| 393_R | 401_L | 1.362 | 0.99 |
| 33_T | 36_V | 1.361 | 0.99 |
| 476_I | 479_E | 1.361 | 0.99 |
| 26_A | 50_Q | 1.350 | 0.99 |
| 214_V | 265_A | 1.346 | 0.99 |
| 476_I | 531_K | 1.345 | 0.99 |
| 69_D | 93_F | 1.342 | 0.99 |
| 382_E | 450_R | 1.340 | 0.99 |
| 343_S | 450_R | 1.339 | 0.99 |
| 121_L | 178_L | 1.335 | 0.99 |
| 536_A | 539_I | 1.323 | 0.99 |
| 65_L | 71_V | 1.321 | 0.99 |
| 36_V | 263_Y | 1.321 | 0.99 |
| 330_A | 339_A | 1.321 | 0.99 |
| 199_N | 338_S | 1.312 | 0.99 |
| 459_D | 471_Y | 1.310 | 0.99 |
| 255_R | 258_D | 1.304 | 0.99 |
| 129_D | 132_L | 1.303 | 0.99 |
| 386_P | 392_I | 1.298 | 0.99 |
| 383_L | 453_L | 1.296 | 0.99 |
| 22_L | 26_A | 1.295 | 0.99 |
| 559_Q | 562_T | 1.291 | 0.99 |
| 214_V | 240_E | 1.287 | 0.99 |
| 410_V | 453_L | 1.287 | 0.99 |
| 390_I | 416_T | 1.281 | 0.99 |
| 72_F | 118_W | 1.281 | 0.99 |
| 96_T | 121_L | 1.279 | 0.99 |
| 393_R | 437_W | 1.276 | 0.99 |
| 300_N | 305_V | 1.271 | 0.99 |
| 37_N | 79_H | 1.271 | 0.99 |
| 177_I | 334_S | 1.270 | 0.99 |
| 521_S | 525_K | 1.268 | 0.99 |
| 190_E | 419_K | 1.263 | 0.99 |
| 71_V | 88_C | 1.262 | 0.99 |
| 19_Q | 193_H | 1.262 | 0.99 |
| 268_T | 295_M | 1.261 | 0.99 |
| 50_Q | 53_A | 1.260 | 0.99 |
| 170_P | 194_R | 1.258 | 0.99 |
| 267_K | 297_C | 1.256 | 0.99 |
| 297_C | 328_R | 1.249 | 0.99 |
| 36_V | 43_T | 1.249 | 0.99 |
| 399_H | 411_Q | 1.246 | 0.98 |
| 216_L | 265_A | 1.242 | 0.98 |
| 49_L | 86_W | 1.238 | 0.98 |
| 482_G | 523_H | 1.229 | 0.98 |
| 103_T | 106_E | 1.227 | 0.98 |
| 190_E | 420_G | 1.226 | 0.98 |
| 116_H | 120_L | 1.221 | 0.98 |
| 213_D | 267_K | 1.218 | 0.98 |
| 53_A | 87_A | 1.214 | 0.98 |
| 175_F | 191_H | 1.205 | 0.98 |
| 407_I | 445_F | 1.205 | 0.98 |
| 392_I | 444_G | 1.199 | 0.98 |
| 119_K | 185_M | 1.198 | 0.98 |
| 474_E | 557_R | 1.197 | 0.98 |
| 343_S | 382_E | 1.197 | 0.98 |
| 189_V | 418_M | 1.196 | 0.98 |
| 42_L | 52_D | 1.196 | 0.98 |
| 249_F | 255_R | 1.196 | 0.98 |
| 273_F | 303_E | 1.192 | 0.98 |
| 116_H | 178_L | 1.189 | 0.98 |
| 44_Q | 49_L | 1.184 | 0.98 |
| 191_H | 418_M | 1.182 | 0.98 |
| 526_S | 530_T | 1.181 | 0.98 |
| 59_G | 62_A | 1.178 | 0.98 |
| 52_D | 55_R | 1.169 | 0.97 |
| 297_C | 326_V | 1.169 | 0.97 |
| 198_A | 415_P | 1.164 | 0.97 |
| 199_N | 339_A | 1.163 | 0.97 |
| 49_L | 83_T | 1.160 | 0.97 |
| 51_G | 55_R | 1.160 | 0.97 |
| 210_T | 213_D | 1.154 | 0.97 |
| 333_M | 438_F | 1.154 | 0.97 |
| 276_A | 279_N | 1.152 | 0.97 |
| 544_K | 547_F | 1.147 | 0.97 |
| 176_F | 188_C | 1.147 | 0.97 |
| 550_T | 556_E | 1.144 | 0.97 |
| 260_M | 294_A | 1.144 | 0.97 |
| 22_L | 86_W | 1.142 | 0.97 |
| 392_I | 410_V | 1.140 | 0.97 |
| 269_W | 339_A | 1.139 | 0.97 |
| 22_L | 50_Q | 1.127 | 0.97 |
| 487_F | 547_F | 1.126 | 0.97 |
| 16_Q | 20_D | 1.113 | 0.96 |
| 271_P | 274_A | 1.112 | 0.96 |
| 336_I | 340_V | 1.112 | 0.96 |
| 199_N | 337_S | 1.111 | 0.96 |
| 387_I | 390_I | 1.105 | 0.96 |
| 191_H | 337_S | 1.101 | 0.96 |
| 402_L | 406_H | 1.098 | 0.96 |
| 247_D | 250_I | 1.096 | 0.96 |
| 393_R | 413_K | 1.096 | 0.96 |
| 527_H | 530_T | 1.094 | 0.96 |
| 394_I | 402_L | 1.092 | 0.96 |
| 547_F | 555_I | 1.088 | 0.96 |
| 409_R | 457_E | 1.085 | 0.96 |
| 75_F | 84_A | 1.085 | 0.96 |
| 48_Q | 51_G | 1.084 | 0.96 |
| 102_P | 105_R | 1.082 | 0.96 |
| 394_I | 451_L | 1.081 | 0.95 |
| 471_Y | 474_E | 1.078 | 0.95 |
| 495_M | 498_S | 1.075 | 0.95 |
| 548_P | 560_L | 1.075 | 0.95 |
| 488_V | 505_L | 1.073 | 0.95 |
| 414_G | 417_T | 1.072 | 0.95 |
| 270_A | 275_F | 1.068 | 0.95 |
| 391_T | 435_D | 1.065 | 0.95 |
| 411_Q | 433_Q | 1.065 | 0.95 |
| 174_V | 193_H | 1.064 | 0.95 |
| 476_I | 528_I | 1.061 | 0.95 |
| 219_M | 225_G | 1.060 | 0.95 |
| 179_T | 189_V | 1.059 | 0.95 |
| 301_G | 339_A | 1.059 | 0.95 |
| 433_Q | 439_H | 1.054 | 0.95 |
| 275_F | 279_N | 1.053 | 0.95 |
| 230_F | 234_N | 1.053 | 0.95 |
| 49_L | 53_A | 1.053 | 0.95 |
| 80_A | 129_D | 1.050 | 0.94 |
| 23_T | 54_E | 1.048 | 0.94 |
| 20_D | 23_T | 1.048 | 0.94 |
| 480_V | 523_H | 1.047 | 0.94 |
| 191_H | 195_S | 1.045 | 0.94 |
| 70_P | 422_Y | 1.045 | 0.94 |
| 21_V | 201_K | 1.044 | 0.94 |
| 305_V | 310_I | 1.044 | 0.94 |
| 522_Q | 526_S | 1.042 | 0.94 |
| 42_L | 80_A | 1.042 | 0.94 |
| 480_V | 524_I | 1.038 | 0.94 |
| 484_E | 508_T | 1.036 | 0.94 |
| 128_T | 132_L | 1.033 | 0.94 |
| 57_L | 90_L | 1.033 | 0.94 |
| 269_W | 330_A | 1.032 | 0.94 |
| 412_I | 440_T | 1.030 | 0.94 |
| 305_V | 327_I | 1.030 | 0.94 |
| 341_V | 451_L | 1.026 | 0.94 |
| 81_M | 221_L | 1.024 | 0.93 |
| 397_H | 457_E | 1.023 | 0.93 |
| 19_Q | 89_V | 1.023 | 0.93 |
| 97_L | 177_I | 1.023 | 0.93 |
| 525_K | 529_A | 1.019 | 0.93 |
| 214_V | 241_Q | 1.016 | 0.93 |
| 295_M | 298_M | 1.012 | 0.93 |
| 30_N | 47_A | 1.009 | 0.93 |
| 238_G | 241_Q | 1.008 | 0.93 |
| 72_F | 121_L | 1.000 | 0.92 |
| 56_V | 84_A | 1.000 | 0.92 |
| 84_A | 88_C | 1.000 | 0.92 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 4r0mB | 2 | 0.9507 | 100 | 0.124 | Contact Map |
| 3tsyA | 1 | 0.7289 | 100 | 0.162 | Contact Map |
| 2vsqA | 1 | 0.8838 | 100 | 0.177 | Contact Map |
| 3etcA | 2 | 0.868 | 100 | 0.181 | Contact Map |
| 3ni2A | 1 | 0.8908 | 100 | 0.181 | Contact Map |
| 3g7sA | 2 | 0.8433 | 100 | 0.188 | Contact Map |
| 3kxwA | 1 | 0.9507 | 100 | 0.19 | Contact Map |
| 2d1sA | 1 | 0.8944 | 100 | 0.19 | Contact Map |
| 1amuA | 2 | 0.8697 | 100 | 0.192 | Contact Map |
| 1pg4A | 2 | 0.919 | 100 | 0.193 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)